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MinKNOW (guppy) not having the permission to basecall or demultiplex from a different location

Hello everyone.

I am still quite new at bioinformatics and I am sorry if this seems like a silly question.

I used Nanopore MinION to sequence a genome, and now I am trying to sequence another genome and I launched MinKNOW for the first time since March.

As a little test run and getting used to MinKNOW again, I decided to basecall some files that I had from March using the new 'super-accuracy' model, but as soon as I set everything in MinKNOW, and move to the Experiments page, nothing is there.

So for some reason I decided to reinstall MinKNOW as per the Nanopore protocol, including doing a full uninstall.

So I am currently on Ubuntu 18.04, in the Host Settings, MinKNOW is 21.06.13, MinKNOW GUI is 4.3.28.

I remember being able to see Guppy's and the API's version too when I hover over the MinKNOW version but maybe it changed in the newer version?

Anyways, even after I reinstalled, I still ran into the same problem.

I checked MinKNOW's log folder, and I took a look at mk_manager_svc_log. I get the following:

2021-11-11 09:19:36.239438    INFO: starting_up (basecall_manager)
    version: 4.3.12
    hostname: user
2021-11-11 09:19:36.244405   ERROR: failed_to_start_crashpad (config)
    message: Failed to find crashpad database
2021-11-11 09:19:36.314636    INFO: manager_notified_new_local_auth_token (util)
    expires_in: 89999862595767ns
2021-11-11 09:40:54.379202    INFO: running_client (basecall_manager)
    executable: /opt/ont/guppy/bin/guppy_basecall_client
    id: 1
    arguments: --port
               5555
               --server_file_load_timeout
               600
               --num_callers=1
               --save_path
               /home2/Genome_sequences/20210506_data/20210421/20211110_basecalling
               --config
               dna_r9.4.1_450bps_sup.cfg
               --input_path
               /home2/Genome_sequences/20210506_data/20210421
               --compress_fastq
               --barcode_kits
               SQK-RBK004
               --trim_barcodes
               --min_score
               60.000000
               --progress_stats_frequency=2
2021-11-11 09:40:54.398641 WARNING: output_unexpectedly_terminated (basecall_manager)
    error: (2:std::asio.misc): [0x0x11338d8]: End of file
    id: 1
2021-11-11 09:40:54.398904   ERROR: analysis_process_failed (basecall_manager)
    exit_code: 255
    output: boost::filesystem::status: Permission denied: "/home2/Genome_sequences/20210506_data/20210421/20211110_basecalling"

I have the suspicion that the problem is because I am directing MinKNOW to a different directory than the default directory, but I do not know how to include the current directory and the default directory (the directory where it is installed by default does not have a lot of memory, so I move old data to a different directory).

If anyone have any idea on why this happens, and if it is possible to allow MinKNOW to basecall from a different directory.

Best regards,

Adham

nanopore guppy minknow
• 11,014 views • link
updated by Abdullah K • Abdullah K • written by adhamzul • adhamzul

I don't have a direct answer for you. Anything ONT can be mysterious and difficult to set up. However, there might be something here that can assist: https://github.com/sirselim . Miles's guides have helped me a lot in the past.

• 0 views • link
written by dr_cfoster dr_cfoster

Remember to back up your data before playing around too much.

Check the permissions on the directory, and all directories above it. Heres a simple guide:

https://opensource.com/article/19/6/understanding-linux-permissions

eg 
cd /home2/Genome_sequences/20210506_data/20210421/20211110_basecalling

ls -l 
cd /home2/Genome_sequences/20210506_data/20210421/
ls -l

Does the user you are running Minknow / guppy as have permissions to write to the directory

sudo su YOUR_MINKNOW_USER
cd /home2/Genome_sequences/20210506_data/20210421/
#create a text file
touch test.txt

# you might then need to change the rights
cd /home2/
sudo chown -R YOUR_MINKNOW_USER *
# grant read and write access to ALL users (can obviously be dangerous, better to set up correctly with users and groups)
sudo chmod -R 777 some_directory

etc. You can change the directories back if you make a mistake.

If all that works, it might be a more sinister problem ...

• 0 views • link
written by colindaven colindaven

Thank you cfos4698 and colindaven for the replies.

I have yet to tinker with things. I was able to successfully run a sequencing run on MinION last week, and MinKNOW was able to save the data to its default directory. But, whenever I try to basecall on MinKNOW from the default data directory, the permission problem persists.

I talked with my supervisor and we decided to try and contact Nanopore for support. Will try and update the thread with the problems and solutions (if available) for the record.

• 0 views • link
written by adhamzul • adhamzul

1 answer

Hey.

I had the same problem, contacted support, and got this!

https://community.nanoporetech.com/support/articles/191

Good luck.

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written by Abdullah K • Abdullah K

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